Entamoeba histolytica is a protozoan parasite that causes tens of millions of cases of dysentery and liver abscess in Latin America, Africa and Asia. Amebiasis liver abscess, which can be lethal if left untreated, is the third leading cause of death due to a parasite. As developing countries cannot afford the improvements in sanitation that might prevent the fecal-oral spread of the parasite, amebiasis is presently poorly controlled by metronidazole-treatment of symptomatic individuals and there is also a need for specific diagnostic tools and vaccines. Whole genome sequencing raises the sophistication and productivity of experimental approaches for studying amebae to a new level. Amebae have four properties, which make them unique among eukaryotic pathogens. First, amebae live under anaerobic conditions in the lumen of the bowel or in tissue abscesses by means of fermentation enzymes like those of bacteria, which are targets of metronidazole. Amebic alcohol dehydrogenases closely resemble those of gram-positive anaerobes, while malic enzyme and ferredoxin resemble those of archaebacteria. Second, amebae have an atrophic, purple bacterium derived organelle ("crypton"), which lacks mitochondrial enzymes of oxidative-phosphorylation and hydrogenosomal fermentation enzymes. Third, amebae phagocytose and lyse host cells by means of adherence lectins, cysteine proteinases, and pore-forming peptides. Fourth, E. histolytica, which causes disease, has a closely related cousin, E. dispar, which infects the colonic lumen but does not cause disease. The study of the E. histolytica genome serves as a model organism for reconstructing the phylogeny of early branching eukaryotes and will also provide insights into the history of anaerobic lumenal parasites. Because of the medical importance of amebae and their unique biology, the goal of this project is to determine 99 percent of the genomic sequence of E. histolytica strain HM1:IMSS, analyze and annotate the data and provide ready equal access to the sequence information and analysis through the public databases and our World Wide Web server (www.tigr.org). The investigators will not attempt closure of the complete sequence of the E. histolytica genome. The haploid genome of HM1 is less than or equal to 20 Mb in 14 chromosomes; amebic genes have rare introns; intergenic sequences are short; and non-coding repetitive sequences are absent from chromosomal DNAs. The vast majority of the research needs and applications will be met by obtaining 99 percent of the genomic sequence.